I removed matheval everywhere in the code. Now, MATHEVAL
(and CUSTOM) keywords are automatically using lepton (see #244).

Notice that env var PLUMED_USE_LEPTON is now ignored.

closes #244

Notice that Lepton is always available but should be triggered with
export PLUMED_USE_LEPTON=yes

Also notice that to behave as matheval it requires defining a pi variable.

[makedoc]

Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

I added an example similar to the one that I provided
on the mailing list about how to mimick
POINT_FROM_AXIS and PROJ_ON_AXIS

[makedoc]

[makedoc]

closes #158

added PERIODIC=NO in the example because this keyword is compulsory.

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

Namespaces are used now in bias/colvar/function/cltools

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

as suggested by Gareth

I added a PEOPLE file containing list of authors and a script
(src/header.sh) which applies the Licence to all the source files.

It can be applies multiple times (it automatically deletes the present header
and replace it with the new one). Thus, to change the header, edit header.sh
and execute it.